def hadesDump1(integrator,
nsample,
xmin,
xmax,
W,
isotopes,
baseFileName,
baseDirectory=".",
mask=None,
dumpGhosts=True,
materials="all"):
# We currently only support 3-D.
assert isinstance(integrator, Spheral.Integrator3d)
assert len(nsample) == 3
assert isinstance(xmin, Spheral.Vector3d)
assert isinstance(xmax, Spheral.Vector3d)
assert isinstance(W, Spheral.TableKernel3d)
for x in isotopes:
for xx in x:
assert len(xx) == 2
# Prepare to time how long this takes.
t0 = time.clock()
# Extract the data base.
db = integrator.dataBase()
# If requested, set ghost node info.
if dumpGhosts and not integrator is None:
state = Spheral.State3d(db, integrator.physicsPackages())
derivs = Spheral.StateDerivatives3d(db, integrator.physicsPackages())
integrator.setGhostNodes()
integrator.applyGhostBoundaries(state, derivs)
# Get the set of material names we're going to write.
if materials == "all":
materials = [n for n in db.fluidNodeLists()]
assert len(materials) == len(isotopes)
# HACK! We are currently restricting to writing single material output!
assert len(materials) == 1
# Make sure the output directory exists.
import mpi
import os
if mpi.rank == 0 and not os.path.exists(baseDirectory):
try:
os.makedirs(baseDirectory)
except:
raise "Cannot create output directory %s" % baseDirectory
mpi.barrier()
# Write the density header file.
print "hadesDump: writing density header..."
if mpi.rank == 0:
filename = os.path.join(baseDirectory, baseFileName + ".spr")
f = open(filename, "w")
f.write("3\n")
for i in xrange(3):
f.write("%i\n" % nsample[i])
f.write("%f\n" % xmin(i))
f.write("%f\n" % ((xmax(i) - xmin(i)) / nsample[i]))
f.write("3\n")
f.close()
mpi.barrier()
# Sample the density.
ntot = nsample[0] * nsample[1] * nsample[2]
for nodes in materials:
print "hadesDump: sampling density for %s..." % nodes.name
r = Spheral.VectorFieldList3d()
H = Spheral.SymTensorFieldList3d()
rho = Spheral.ScalarFieldList3d()
r.appendField(nodes.positions())
w.appendField(nodes.weight())
H.appendField(nodes.Hfield())
rho.appendField(nodes.massDensity())
w = Spheral.ScalarFieldList3d()
w.copyFields()
w.appendField(Spheral.ScalarField3d("weight", nodes, 1.0))
fieldListSet = Spheral.FieldListSet3d()
fieldListSet.ScalarFieldLists.append(rho)
localMask = Spheral.IntFieldList3d()
if mask is None:
localMask.copyFields()
localMask.appendField(Spheral.IntField3d("mask", nodes, 1))
else:
localMask.appendField(mask.fieldForNodeList(nodes))
scalar_samples = Spheral.vector_of_vector_of_double()
vector_samples = Spheral.vector_of_vector_of_Vector3d()
tensor_samples = Spheral.vector_of_vector_of_Tensor3d()
symTensor_samples = Spheral.vector_of_vector_of_SymTensor3d()
nsample_vec = Spheral.vector_of_int(3)
for i in xrange(3):
nsample_vec[i] = nsample[i]
Spheral.sampleMultipleFields2Lattice3d(fieldListSet, r, w, H,
localMask, W, xmin, xmax,
nsample_vec, scalar_samples,
vector_samples, tensor_samples,
symTensor_samples)
print "Generated %i scalar fields" % len(scalar_samples)
rhosamp = scalar_fields[0]
nlocal = len(rhosamp)
assert mpi.allreduce(nlocal, mpi.SUM) == ntot
print "hadesDump: writing density for %s..." % nodes.name
filename = os.path.join(baseDirectory, baseFileName + ".sdt")
for sendProc in xrange(mpi.procs):
if mpi.rank == sendProc:
f = open(filename, "ab")
f.write(struct.pack(nlocal * "f", *tuple(rhosamp)))
f.close()
mpi.barrier()
# Write the material arrays.
print "hadesDump: writing material flags..."
filename = os.path.join(baseDirectory, baseFileName + "_mat.sdt")
for sendProc in xrange(mpi.procs):
if mpi.rank == sendProc:
f = open(filename, "ab")
f.write(struct.pack(nlocal * "i", *(nlocal * (1, ))))
f.close()
mpi.barrier()
# Write the isotopes.
print "hadesDump: writing isotopics..."
if mpi.rank == 0:
filename = os.path.join(baseDirectory, "isos.mat")
f = open(filename, "w")
i = 0
for isofracs in isotopes:
f.write("isofrac(%i) =" % i)
for (iso, frac) in isofracs:
f.write(" %i %f" % (iso, frac))
f.write("\n")
i += 1
f.close()
mpi.barrier()
mpi.barrier()
print "hadesDump finished: required %0.2f seconds" % (time.clock() - t0)
return
def hadesDump0(integrator,
nsample,
xmin,
xmax,
W,
isotopes,
baseFileName,
baseDirectory=".",
dumpGhosts=False,
materials="all"):
# We currently only support 3-D.
assert isinstance(integrator, Spheral.Integrator3d)
assert len(nsample) == 3
assert isinstance(xmin, Spheral.Vector3d)
assert isinstance(xmax, Spheral.Vector3d)
assert isinstance(W, Spheral.TableKernel3d)
for x in isotopes:
for xx in x:
assert len(xx) == 2
# Prepare to time how long this takes.
t0 = time.clock()
# Extract the data base.
db = integrator.dataBase()
# If requested, set ghost node info.
if dumpGhosts and not integrator is None:
state = Spheral.State3d(db, integrator.physicsPackages())
derivs = Spheral.StateDerivatives3d(db, integrator.physicsPackages())
integrator.setGhostNodes()
integrator.applyGhostBoundaries(state, derivs)
# Get the set of material names we're going to write.
if materials == "all":
materials = [n for n in db.fluidNodeLists()]
assert len(materials) == len(isotopes)
# Make sure the output directory exists.
import mpi
import os
if mpi.rank == 0 and not os.path.exists(baseDirectory):
try:
os.makedirs(baseDirectory)
except:
raise "Cannot create output directory %s" % baseDirectory
mpi.barrier()
# Open a file for the output.
currentTime = integrator.currentTime
currentCycle = integrator.currentCycle
filename = baseDirectory + "/" + baseFileName + "-time=%g-cycle=%i.hades" % (
currentTime, currentCycle)
if mpi.rank == 0:
f = open(filename, "wb")
# Write the header info.
#f.write(hadesHeader)
f.write(struct.pack("I", len(materials)))
f.write(struct.pack("ddd", *tuple(xmin.elements())))
f.write(struct.pack("ddd", *tuple(xmax.elements())))
f.write(struct.pack("III", *nsample))
for materialIsotopes in isotopes:
f.write(struct.pack("I", len(materialIsotopes)))
for iso in materialIsotopes:
f.write(struct.pack("Id", *iso))
# For each material, sample the mass density and write it out.
ntot = nsample[0] * nsample[1] * nsample[2]
for nodes in materials:
r = Spheral.VectorFieldList3d()
w = Spheral.ScalarFieldList3d()
H = Spheral.SymTensorFieldList3d()
rho = Spheral.ScalarFieldList3d()
r.appendField(nodes.positions())
w.appendField(nodes.weight())
H.appendField(nodes.Hfield())
rho.appendField(nodes.massDensity())
fieldListSet = Spheral.FieldListSet3d()
fieldListSet.ScalarFieldLists.append(rho)
rhosamp = Spheral.sampleMultipleFields2LatticeMash(
fieldListSet, r, w, H, W, xmin, xmax, nsample)[0][0][1]
assert mpi.allreduce(len(rhosamp), mpi.SUM) == ntot
icum = 0
for sendProc in xrange(mpi.procs):
valsproc = [(i, x) for (i, x) in zip(range(ntot), rhosamp)
if x > 0.0]
vals = mpi.bcast(valsproc, sendProc)
if mpi.rank == 0:
f.write(struct.pack("I", len(vals)))
for i, x in vals:
f.write(struct.pack("id", i + icum, x))
icum += len(vals)
if mpi.rank == 0:
# Close the file and we're done.
f.close()
mpi.barrier()
print "hadesDump finished: required %0.2f seconds" % (time.clock() - t0)
return